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Relationship between histone modifications and transcription factor binding is protein family specific

Genome research, 2018-03, Vol.28 (3), p.321-333

2018

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Predicting DNA structure using a deep learning method

Nature communications, 2024-02, Vol.15 (1), p.1243-1243, Article 1243

2024

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Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

Molecular cell, 2014-06, Vol.54 (5), p.844-857

2014

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ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Nature communications, 2015-10, Vol.6 (1), p.8733-8733, Article 8733

2015

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DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes

Nucleic acids research, 2020-01, Vol.48 (D1), p.D277

2020

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Genome information processing by the INO80 chromatin remodeler positions nucleosomes

Nature communications, 2021-05, Vol.12 (1), p.3231-3231, Article 3231

2021

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The role of DNA shape in protein-DNA recognition

Nature (London), 2009-10, Vol.461 (7268), p.1248-1253

2009

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Origins of specificity in protein-DNA recognition

Annual review of biochemistry, 2010-01, Vol.79 (1), p.233-269

2010

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Quantum annealing versus classical machine learning applied to a simplified computational biology problem

npj quantum information, 2018-02, Vol.4 (1), p.1-10, Article 14

2018

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A widespread role of the motif environment in transcription factor binding across diverse protein families

Genome research, 2015-09, Vol.25 (9), p.1268-1280

2015

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DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

Bioinformatics, 2016-04, Vol.32 (8), p.1211-1213

2016

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TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites

Nucleic acids research, 2020-01, Vol.48 (D1), p.D246

2020

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DNAproDB: an interactive tool for structural analysis of DNA-protein complexes

Nucleic acids research, 2017-07, Vol.45 (W1), p.W89-W97

2017

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Humanizing the yeast origin recognition complex

Nature communications, 2021-01, Vol.12 (1), p.33-33, Article 33

2021

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Quantitative modeling of transcription factor binding specificities using DNA shape

Proceedings of the National Academy of Sciences - PNAS, 2015-04, Vol.112 (15), p.4654-4659

2015

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Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding

Nucleic acids research, 2017-12, Vol.45 (22), p.12877-12887

2017

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Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

Cell reports (Cambridge), 2013-04, Vol.3 (4), p.1093-1104

2013

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DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

Nucleic acids research, 2013-07, Vol.41 (Web Server issue), p.W56-W62

2013

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Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

Cell, 2011-12, Vol.147 (6), p.1270-1282

2011

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Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

Molecular systems biology, 2017-02, Vol.13 (2), p.910-n/a

2017

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How motif environment influences transcription factor search dynamics: Finding a needle in a haystack

BioEssays, 2016-07, Vol.38 (7), p.605-612

2016

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Unraveling determinants of transcription factor binding outside the core binding site

Genome research, 2015-07, Vol.25 (7), p.1018-1029

2015

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TFBSshape: a motif database for DNA shape features of transcription factor binding sites

Nucleic acids research, 2014-01, Vol.42 (Database issue), p.D148-D155

2014

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High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

Cell reports (Cambridge), 2015-05, Vol.11 (5), p.821-834

2015

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Probing DNA shape and methylation state on a genomic scale with DNase I

Proceedings of the National Academy of Sciences - PNAS, 2013-04, Vol.110 (16), p.6376-6381

2013

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Relationship between histone modifications and transcription factor binding is protein family specific

Predicting DNA structure using a deep learning method

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes

Genome information processing by the INO80 chromatin remodeler positions nucleosomes

The role of DNA shape in protein-DNA recognition

Origins of specificity in protein-DNA recognition

Quantum annealing versus classical machine learning applied to a simplified computational biology problem

A widespread role of the motif environment in transcription factor binding across diverse protein families

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites

DNAproDB: an interactive tool for structural analysis of DNA-protein complexes

Humanizing the yeast origin recognition complex

Quantitative modeling of transcription factor binding specificities using DNA shape

Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

How motif environment influences transcription factor search dynamics: Finding a needle in a haystack

Unraveling determinants of transcription factor binding outside the core binding site

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

Probing DNA shape and methylation state on a genomic scale with DNase I

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